Starting phenix.real_space_refine on Sat Jul 4 01:16:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqr_36577/07_2026/8jqr_36577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqr_36577/07_2026/8jqr_36577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jqr_36577/07_2026/8jqr_36577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqr_36577/07_2026/8jqr_36577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jqr_36577/07_2026/8jqr_36577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqr_36577/07_2026/8jqr_36577.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.133 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11476 2.51 5 N 2784 2.21 5 O 3064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17444 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "B" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "C" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'EZI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'EZI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'EZI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'EZI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.59, per 1000 atoms: 0.21 Number of scatterers: 17444 At special positions: 0 Unit cell: (122.72, 123.76, 110.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3064 8.00 N 2784 7.00 C 11476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 457.2 milliseconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 65.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.539A pdb=" N ILE A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.596A pdb=" N LYS A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 Processing helix chain 'A' and resid 346 through 355 removed outlier: 3.664A pdb=" N TYR A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.703A pdb=" N LEU A 414 " --> pdb=" O HIS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.798A pdb=" N ARG A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 455 Processing helix chain 'A' and resid 469 through 500 removed outlier: 3.557A pdb=" N VAL A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.517A pdb=" N TYR A 555 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 576 through 599 Processing helix chain 'A' and resid 630 through 643 removed outlier: 3.896A pdb=" N PHE A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'A' and resid 674 through 691 Processing helix chain 'A' and resid 693 through 714 Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.543A pdb=" N ILE B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 261 through 271 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 299 through 321 removed outlier: 3.597A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.662A pdb=" N TYR B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.722A pdb=" N LEU B 414 " --> pdb=" O HIS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 430 removed outlier: 3.796A pdb=" N ARG B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 430 " --> pdb=" O LYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 455 Processing helix chain 'B' and resid 469 through 500 Processing helix chain 'B' and resid 510 through 531 Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.517A pdb=" N TYR B 555 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 576 through 599 Processing helix chain 'B' and resid 630 through 643 removed outlier: 3.878A pdb=" N PHE B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 674 through 691 Processing helix chain 'B' and resid 693 through 714 Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.544A pdb=" N ILE C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 224 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 299 through 321 removed outlier: 3.598A pdb=" N LYS C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 346 through 355 removed outlier: 3.669A pdb=" N TYR C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.716A pdb=" N LEU C 414 " --> pdb=" O HIS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 430 removed outlier: 3.795A pdb=" N ARG C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 455 Processing helix chain 'C' and resid 469 through 500 Processing helix chain 'C' and resid 510 through 532 removed outlier: 3.547A pdb=" N MET C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.513A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 559 through 576 Processing helix chain 'C' and resid 576 through 599 removed outlier: 3.572A pdb=" N ALA C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 643 removed outlier: 3.876A pdb=" N PHE C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR C 642 " --> pdb=" O LEU C 638 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 643 " --> pdb=" O PHE C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'C' and resid 674 through 691 Processing helix chain 'C' and resid 693 through 714 Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.545A pdb=" N ILE D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 251 through 259 Processing helix chain 'D' and resid 261 through 271 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 299 through 321 removed outlier: 3.604A pdb=" N LYS D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 345 Processing helix chain 'D' and resid 346 through 355 removed outlier: 3.668A pdb=" N TYR D 352 " --> pdb=" O GLY D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 367 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 411 through 415 removed outlier: 3.690A pdb=" N LEU D 414 " --> pdb=" O HIS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 430 removed outlier: 3.789A pdb=" N ARG D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 455 Processing helix chain 'D' and resid 469 through 500 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.530A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 576 through 599 removed outlier: 3.582A pdb=" N ALA D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.880A pdb=" N PHE D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 672 Processing helix chain 'D' and resid 674 through 691 Processing helix chain 'D' and resid 693 through 714 Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 374 removed outlier: 3.757A pdb=" N TRP A 373 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASP A 738 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 729 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 740 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 371 through 374 removed outlier: 7.053A pdb=" N SER B 380 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA B 374 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASP B 738 " --> pdb=" O VAL B 729 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 729 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 740 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 371 through 374 removed outlier: 7.060A pdb=" N SER C 380 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA C 374 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASP C 738 " --> pdb=" O VAL C 729 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 729 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 740 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 373 through 374 removed outlier: 3.794A pdb=" N TRP D 373 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASP D 738 " --> pdb=" O VAL D 729 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 729 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 740 " --> pdb=" O LEU D 727 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 2684 1.26 - 1.40: 4789 1.40 - 1.54: 9857 1.54 - 1.67: 342 1.67 - 1.81: 204 Bond restraints: 17876 Sorted by residual: bond pdb=" C08 EZI B1201 " pdb=" C09 EZI B1201 " ideal model delta sigma weight residual 1.446 1.349 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C08 EZI D1201 " pdb=" C09 EZI D1201 " ideal model delta sigma weight residual 1.446 1.350 0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C22 EZI D1201 " pdb=" C23 EZI D1201 " ideal model delta sigma weight residual 1.428 1.524 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C22 EZI C1201 " pdb=" C23 EZI C1201 " ideal model delta sigma weight residual 1.428 1.524 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C22 EZI B1201 " pdb=" C23 EZI B1201 " ideal model delta sigma weight residual 1.428 1.524 -0.096 2.00e-02 2.50e+03 2.29e+01 ... (remaining 17871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 23409 1.41 - 2.82: 637 2.82 - 4.23: 123 4.23 - 5.64: 32 5.64 - 7.05: 15 Bond angle restraints: 24216 Sorted by residual: angle pdb=" N VAL D 729 " pdb=" CA VAL D 729 " pdb=" C VAL D 729 " ideal model delta sigma weight residual 112.96 109.81 3.15 1.00e+00 1.00e+00 9.92e+00 angle pdb=" N VAL B 729 " pdb=" CA VAL B 729 " pdb=" C VAL B 729 " ideal model delta sigma weight residual 112.96 109.85 3.11 1.00e+00 1.00e+00 9.66e+00 angle pdb=" N VAL A 729 " pdb=" CA VAL A 729 " pdb=" C VAL A 729 " ideal model delta sigma weight residual 112.96 109.87 3.09 1.00e+00 1.00e+00 9.53e+00 angle pdb=" N VAL C 729 " pdb=" CA VAL C 729 " pdb=" C VAL C 729 " ideal model delta sigma weight residual 112.96 109.89 3.07 1.00e+00 1.00e+00 9.44e+00 angle pdb=" N PHE B 305 " pdb=" CA PHE B 305 " pdb=" C PHE B 305 " ideal model delta sigma weight residual 110.97 113.73 -2.76 1.09e+00 8.42e-01 6.41e+00 ... (remaining 24211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 9412 13.87 - 27.74: 896 27.74 - 41.62: 279 41.62 - 55.49: 68 55.49 - 69.36: 21 Dihedral angle restraints: 10676 sinusoidal: 4432 harmonic: 6244 Sorted by residual: dihedral pdb=" CA TYR C 654 " pdb=" C TYR C 654 " pdb=" N ASP C 655 " pdb=" CA ASP C 655 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TYR B 654 " pdb=" C TYR B 654 " pdb=" N ASP B 655 " pdb=" CA ASP B 655 " ideal model delta harmonic sigma weight residual 180.00 158.77 21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA TYR A 654 " pdb=" C TYR A 654 " pdb=" N ASP A 655 " pdb=" CA ASP A 655 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 10673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1710 0.032 - 0.064: 756 0.064 - 0.096: 195 0.096 - 0.128: 48 0.128 - 0.161: 7 Chirality restraints: 2716 Sorted by residual: chirality pdb=" C14 CLR D1202 " pdb=" C13 CLR D1202 " pdb=" C15 CLR D1202 " pdb=" C8 CLR D1202 " both_signs ideal model delta sigma weight residual False -2.32 -2.48 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" C14 CLR A1202 " pdb=" C13 CLR A1202 " pdb=" C15 CLR A1202 " pdb=" C8 CLR A1202 " both_signs ideal model delta sigma weight residual False -2.32 -2.47 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" C14 CLR C1202 " pdb=" C13 CLR C1202 " pdb=" C15 CLR C1202 " pdb=" C8 CLR C1202 " both_signs ideal model delta sigma weight residual False -2.32 -2.47 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 2713 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 656 " -0.021 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 656 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 656 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 656 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 656 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 656 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 656 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 656 " -0.019 2.00e-02 2.50e+03 1.62e-02 4.57e+00 pdb=" CG PHE B 656 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 656 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 656 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 656 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 656 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 656 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 407 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 408 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " -0.021 5.00e-02 4.00e+02 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4281 2.79 - 3.31: 16762 3.31 - 3.84: 28842 3.84 - 4.37: 36631 4.37 - 4.90: 59834 Nonbonded interactions: 146350 Sorted by model distance: nonbonded pdb=" O THR D 593 " pdb=" OG1 THR D 597 " model vdw 2.256 3.040 nonbonded pdb=" O LEU A 255 " pdb=" OG1 THR A 259 " model vdw 2.279 3.040 nonbonded pdb=" NH1 ARG D 364 " pdb=" O VAL D 729 " model vdw 2.285 3.120 nonbonded pdb=" OH TYR B 584 " pdb=" OG1 THR B 642 " model vdw 2.289 3.040 nonbonded pdb=" O THR C 593 " pdb=" OG1 THR C 597 " model vdw 2.297 3.040 ... (remaining 146345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.180 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 17876 Z= 0.217 Angle : 0.590 7.048 24216 Z= 0.313 Chirality : 0.038 0.161 2716 Planarity : 0.004 0.039 2956 Dihedral : 12.752 69.360 6668 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.17), residues: 2108 helix: -0.16 (0.14), residues: 1236 sheet: -0.72 (0.58), residues: 84 loop : -1.49 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 740 TYR 0.009 0.001 TYR B 584 PHE 0.039 0.002 PHE A 656 TRP 0.014 0.001 TRP C 698 HIS 0.004 0.001 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 (17876) covalent geometry : angle 0.58964 / 0.31 (24216) hydrogen bonds : bond 0.23599 / 15.54 ( 1014) hydrogen bonds : angle 7.53273 / 5.42 ( 2940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 581 MET cc_start: 0.7994 (mmm) cc_final: 0.7694 (mmm) REVERT: B 581 MET cc_start: 0.8050 (mmm) cc_final: 0.7768 (mmm) REVERT: C 465 LYS cc_start: 0.7366 (mmtm) cc_final: 0.6808 (mmmm) REVERT: C 581 MET cc_start: 0.8144 (mmm) cc_final: 0.7866 (mmm) REVERT: D 581 MET cc_start: 0.7884 (mmm) cc_final: 0.7615 (mmm) REVERT: D 678 MET cc_start: 0.8009 (ttt) cc_final: 0.7736 (ttm) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.6540 time to fit residues: 200.1648 Evaluate side-chains 216 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 411 HIS B 207 HIS B 411 HIS C 207 HIS C 411 HIS D 207 HIS D 411 HIS D 688 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.215969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.161515 restraints weight = 15534.173| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.29 r_work: 0.3400 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17876 Z= 0.135 Angle : 0.550 7.984 24216 Z= 0.296 Chirality : 0.037 0.126 2716 Planarity : 0.004 0.038 2956 Dihedral : 5.007 53.289 2624 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.64 % Allowed : 8.30 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2108 helix: 1.15 (0.14), residues: 1264 sheet: -1.59 (0.47), residues: 116 loop : -1.40 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 499 TYR 0.010 0.001 TYR B 200 PHE 0.017 0.002 PHE B 496 TRP 0.014 0.001 TRP C 698 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (17876) covalent geometry : angle 0.54960 / 0.30 (24216) hydrogen bonds : bond 0.05092 / 3.37 ( 1014) hydrogen bonds : angle 4.63642 / 3.29 ( 2940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 286 ASN cc_start: 0.7637 (m-40) cc_final: 0.7402 (t0) REVERT: A 581 MET cc_start: 0.8627 (mmm) cc_final: 0.8203 (tpt) REVERT: A 683 MET cc_start: 0.9174 (mtt) cc_final: 0.8773 (mtt) REVERT: B 286 ASN cc_start: 0.7710 (m-40) cc_final: 0.7418 (t0) REVERT: B 581 MET cc_start: 0.8651 (mmm) cc_final: 0.8236 (tpt) REVERT: B 683 MET cc_start: 0.9120 (mtt) cc_final: 0.8699 (mtt) REVERT: C 286 ASN cc_start: 0.7712 (m-40) cc_final: 0.7428 (t0) REVERT: C 465 LYS cc_start: 0.7536 (mmtm) cc_final: 0.6838 (mmmm) REVERT: C 478 GLU cc_start: 0.7060 (tt0) cc_final: 0.6804 (tt0) REVERT: C 514 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7806 (tmt) REVERT: C 581 MET cc_start: 0.8609 (mmm) cc_final: 0.8197 (tpt) REVERT: C 683 MET cc_start: 0.9162 (mtt) cc_final: 0.8772 (mtt) REVERT: D 286 ASN cc_start: 0.7687 (m-40) cc_final: 0.7377 (t0) REVERT: D 581 MET cc_start: 0.8603 (mmm) cc_final: 0.8213 (tpt) REVERT: D 678 MET cc_start: 0.8522 (ttt) cc_final: 0.8248 (ttm) REVERT: D 683 MET cc_start: 0.9161 (mtt) cc_final: 0.8770 (mtt) REVERT: D 693 GLU cc_start: 0.7190 (pt0) cc_final: 0.6967 (pt0) outliers start: 12 outliers final: 4 residues processed: 245 average time/residue: 0.5941 time to fit residues: 161.3684 Evaluate side-chains 215 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 210 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 130 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 HIS A 688 ASN B 411 HIS B 688 ASN C 411 HIS C 688 ASN D 411 HIS D 498 GLN D 688 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.214376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.160736 restraints weight = 15740.663| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.36 r_work: 0.3346 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17876 Z= 0.155 Angle : 0.543 7.156 24216 Z= 0.289 Chirality : 0.038 0.121 2716 Planarity : 0.004 0.038 2956 Dihedral : 5.147 55.563 2624 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.09 % Allowed : 10.60 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2108 helix: 1.59 (0.14), residues: 1268 sheet: -1.84 (0.46), residues: 116 loop : -1.43 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 499 TYR 0.011 0.001 TYR D 310 PHE 0.018 0.002 PHE D 305 TRP 0.015 0.001 TRP A 698 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (17876) covalent geometry : angle 0.54266 / 0.29 (24216) hydrogen bonds : bond 0.04726 / 3.15 ( 1014) hydrogen bonds : angle 4.38728 / 3.10 ( 2940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.454 Fit side-chains REVERT: A 255 LEU cc_start: 0.6455 (mt) cc_final: 0.6233 (mt) REVERT: A 581 MET cc_start: 0.8709 (mmm) cc_final: 0.8399 (mmm) REVERT: A 693 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7122 (pt0) REVERT: B 286 ASN cc_start: 0.7645 (m-40) cc_final: 0.7364 (t0) REVERT: B 581 MET cc_start: 0.8730 (mmm) cc_final: 0.8294 (tpt) REVERT: B 683 MET cc_start: 0.9177 (mtt) cc_final: 0.8770 (mtt) REVERT: C 255 LEU cc_start: 0.6503 (mt) cc_final: 0.6267 (mt) REVERT: C 286 ASN cc_start: 0.7680 (m-40) cc_final: 0.7389 (t0) REVERT: C 465 LYS cc_start: 0.7487 (mmtm) cc_final: 0.6775 (mmmm) REVERT: C 514 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7894 (tmt) REVERT: C 581 MET cc_start: 0.8666 (mmm) cc_final: 0.8228 (tpt) REVERT: C 683 MET cc_start: 0.9182 (mtt) cc_final: 0.8802 (mtt) REVERT: D 255 LEU cc_start: 0.6525 (mt) cc_final: 0.6285 (mt) REVERT: D 286 ASN cc_start: 0.7661 (m-40) cc_final: 0.7335 (t0) REVERT: D 581 MET cc_start: 0.8711 (mmm) cc_final: 0.8281 (tpt) outliers start: 39 outliers final: 12 residues processed: 243 average time/residue: 0.5974 time to fit residues: 161.2503 Evaluate side-chains 219 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 14 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 163 optimal weight: 0.2980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 HIS A 688 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 HIS B 688 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS C 688 ASN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 688 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.213823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161147 restraints weight = 15640.155| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.32 r_work: 0.3353 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17876 Z= 0.167 Angle : 0.546 5.792 24216 Z= 0.291 Chirality : 0.038 0.121 2716 Planarity : 0.004 0.039 2956 Dihedral : 5.232 57.876 2624 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.50 % Allowed : 14.13 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2108 helix: 1.66 (0.14), residues: 1272 sheet: -1.91 (0.45), residues: 116 loop : -1.54 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 722 TYR 0.012 0.001 TYR D 584 PHE 0.018 0.002 PHE D 305 TRP 0.015 0.001 TRP A 698 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (17876) covalent geometry : angle 0.54597 / 0.29 (24216) hydrogen bonds : bond 0.04682 / 3.12 ( 1014) hydrogen bonds : angle 4.33643 / 3.06 ( 2940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.624 Fit side-chains REVERT: A 255 LEU cc_start: 0.6483 (mt) cc_final: 0.6204 (mt) REVERT: A 315 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6257 (mpt) REVERT: A 472 TYR cc_start: 0.8238 (m-80) cc_final: 0.8003 (m-80) REVERT: A 581 MET cc_start: 0.8647 (mmm) cc_final: 0.8321 (mmm) REVERT: A 693 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7189 (pt0) REVERT: B 255 LEU cc_start: 0.6562 (mt) cc_final: 0.6292 (mt) REVERT: B 581 MET cc_start: 0.8718 (mmm) cc_final: 0.8402 (mmm) REVERT: C 255 LEU cc_start: 0.6550 (mt) cc_final: 0.6281 (mt) REVERT: C 286 ASN cc_start: 0.7628 (m-40) cc_final: 0.7327 (t0) REVERT: C 465 LYS cc_start: 0.7487 (mmtm) cc_final: 0.6750 (mmmm) REVERT: C 514 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7825 (tmt) REVERT: C 581 MET cc_start: 0.8641 (mmm) cc_final: 0.8253 (tpt) REVERT: D 255 LEU cc_start: 0.6556 (mt) cc_final: 0.6285 (mt) REVERT: D 581 MET cc_start: 0.8635 (mmm) cc_final: 0.8305 (mmm) outliers start: 28 outliers final: 20 residues processed: 230 average time/residue: 0.6144 time to fit residues: 156.5226 Evaluate side-chains 219 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 712 SER Chi-restraints excluded: chain D residue 742 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 162 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 195 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 HIS A 688 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 HIS B 688 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 688 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.210301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153906 restraints weight = 15577.107| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.40 r_work: 0.3278 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17876 Z= 0.296 Angle : 0.665 7.943 24216 Z= 0.349 Chirality : 0.044 0.150 2716 Planarity : 0.005 0.044 2956 Dihedral : 5.769 48.119 2624 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.94 % Allowed : 14.08 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2108 helix: 0.99 (0.14), residues: 1292 sheet: -2.14 (0.44), residues: 116 loop : -1.57 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 722 TYR 0.016 0.002 TYR D 584 PHE 0.022 0.003 PHE C 650 TRP 0.018 0.002 TRP D 698 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.30 (17876) covalent geometry : angle 0.66456 / 0.35 (24216) hydrogen bonds : bond 0.05681 / 3.82 ( 1014) hydrogen bonds : angle 4.59769 / 3.24 ( 2940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 255 LEU cc_start: 0.6372 (mt) cc_final: 0.6068 (mt) REVERT: A 315 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6204 (mpt) REVERT: A 581 MET cc_start: 0.8738 (mmm) cc_final: 0.8418 (mmm) REVERT: B 255 LEU cc_start: 0.6747 (mt) cc_final: 0.6418 (mt) REVERT: B 581 MET cc_start: 0.8737 (mmm) cc_final: 0.8429 (mmm) REVERT: C 255 LEU cc_start: 0.6808 (mt) cc_final: 0.6507 (mt) REVERT: C 503 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6871 (tpt) REVERT: C 541 MET cc_start: 0.8923 (ttp) cc_final: 0.8710 (ttp) REVERT: C 581 MET cc_start: 0.8715 (mmm) cc_final: 0.8417 (mmm) REVERT: D 255 LEU cc_start: 0.6758 (mt) cc_final: 0.6429 (mt) REVERT: D 503 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6708 (tpt) REVERT: D 581 MET cc_start: 0.8739 (mmm) cc_final: 0.8450 (mmm) outliers start: 55 outliers final: 29 residues processed: 244 average time/residue: 0.5885 time to fit residues: 160.3457 Evaluate side-chains 236 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 712 SER Chi-restraints excluded: chain D residue 742 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 208 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS A 688 ASN B 261 GLN B 411 HIS B 688 ASN C 261 GLN C 411 HIS C 688 ASN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 688 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.214372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.161421 restraints weight = 15596.091| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.47 r_work: 0.3344 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17876 Z= 0.137 Angle : 0.525 5.885 24216 Z= 0.280 Chirality : 0.037 0.120 2716 Planarity : 0.004 0.041 2956 Dihedral : 5.183 49.595 2624 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.77 % Allowed : 15.26 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2108 helix: 1.75 (0.14), residues: 1268 sheet: -2.07 (0.44), residues: 116 loop : -1.67 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 722 TYR 0.009 0.001 TYR D 584 PHE 0.017 0.001 PHE D 305 TRP 0.015 0.001 TRP B 698 HIS 0.004 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (17876) covalent geometry : angle 0.52517 / 0.28 (24216) hydrogen bonds : bond 0.04336 / 2.90 ( 1014) hydrogen bonds : angle 4.27011 / 3.01 ( 2940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 255 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6005 (mt) REVERT: A 315 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6455 (mmm) REVERT: A 581 MET cc_start: 0.8634 (mmm) cc_final: 0.8288 (mmm) REVERT: B 255 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5975 (mt) REVERT: B 478 GLU cc_start: 0.6113 (tt0) cc_final: 0.5696 (mt-10) REVERT: B 581 MET cc_start: 0.8643 (mmm) cc_final: 0.8270 (tpt) REVERT: C 255 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5942 (mt) REVERT: C 333 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.7004 (tppt) REVERT: C 478 GLU cc_start: 0.6181 (tt0) cc_final: 0.5753 (tt0) REVERT: C 514 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.8028 (pp-130) REVERT: C 581 MET cc_start: 0.8613 (mmm) cc_final: 0.8220 (tpt) REVERT: D 255 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.5980 (mt) REVERT: D 478 GLU cc_start: 0.6113 (tt0) cc_final: 0.5693 (mt-10) REVERT: D 581 MET cc_start: 0.8622 (mmm) cc_final: 0.8230 (tpt) outliers start: 33 outliers final: 16 residues processed: 233 average time/residue: 0.6176 time to fit residues: 160.1904 Evaluate side-chains 215 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 712 SER Chi-restraints excluded: chain D residue 742 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 151 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 173 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 HIS A 688 ASN B 411 HIS B 688 ASN C 411 HIS C 688 ASN D 261 GLN D 411 HIS D 688 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.213420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.3751 r_free = 0.3751 target = 0.157184 restraints weight = 15641.292| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.41 r_work: 0.3326 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17876 Z= 0.167 Angle : 0.553 6.365 24216 Z= 0.293 Chirality : 0.038 0.122 2716 Planarity : 0.004 0.041 2956 Dihedral : 5.250 44.140 2624 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.87 % Allowed : 16.33 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2108 helix: 1.72 (0.14), residues: 1268 sheet: -2.14 (0.44), residues: 116 loop : -1.66 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.012 0.001 TYR A 584 PHE 0.018 0.002 PHE D 305 TRP 0.016 0.002 TRP B 698 HIS 0.008 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (17876) covalent geometry : angle 0.55266 / 0.29 (24216) hydrogen bonds : bond 0.04605 / 3.08 ( 1014) hydrogen bonds : angle 4.27199 / 3.01 ( 2940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.499 Fit side-chains REVERT: A 255 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.5980 (mt) REVERT: A 581 MET cc_start: 0.8675 (mmm) cc_final: 0.8365 (mmm) REVERT: B 255 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5968 (mt) REVERT: B 315 MET cc_start: 0.6999 (mmm) cc_final: 0.6795 (mmt) REVERT: B 478 GLU cc_start: 0.5966 (tt0) cc_final: 0.5429 (tt0) REVERT: B 581 MET cc_start: 0.8690 (mmm) cc_final: 0.8377 (mmm) REVERT: C 255 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6047 (mt) REVERT: C 333 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6621 (tppt) REVERT: C 472 TYR cc_start: 0.8206 (m-80) cc_final: 0.8003 (m-80) REVERT: C 478 GLU cc_start: 0.6216 (tt0) cc_final: 0.5721 (mt-10) REVERT: C 581 MET cc_start: 0.8665 (mmm) cc_final: 0.8305 (tpt) REVERT: D 255 LEU cc_start: 0.6422 (mt) cc_final: 0.5995 (mt) REVERT: D 465 LYS cc_start: 0.7389 (mptt) cc_final: 0.6441 (mmmm) REVERT: D 472 TYR cc_start: 0.8180 (m-80) cc_final: 0.7970 (m-80) REVERT: D 478 GLU cc_start: 0.5950 (tt0) cc_final: 0.5567 (mt-10) REVERT: D 503 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6607 (tpt) REVERT: D 581 MET cc_start: 0.8671 (mmm) cc_final: 0.8311 (tpt) outliers start: 35 outliers final: 23 residues processed: 228 average time/residue: 0.5713 time to fit residues: 145.5101 Evaluate side-chains 227 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 712 SER Chi-restraints excluded: chain D residue 742 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 86 optimal weight: 0.0670 chunk 169 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 99 optimal weight: 0.0980 chunk 125 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 202 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 HIS A 688 ASN B 411 HIS B 688 ASN C 270 GLN C 411 HIS C 688 ASN D 411 HIS D 688 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.217422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162837 restraints weight = 15579.362| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.44 r_work: 0.3379 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17876 Z= 0.108 Angle : 0.496 6.940 24216 Z= 0.263 Chirality : 0.035 0.119 2716 Planarity : 0.003 0.039 2956 Dihedral : 4.853 43.001 2624 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.34 % Allowed : 16.97 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 2108 helix: 2.11 (0.14), residues: 1280 sheet: -2.05 (0.44), residues: 116 loop : -1.45 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.008 0.001 TYR A 310 PHE 0.019 0.001 PHE D 305 TRP 0.013 0.001 TRP D 698 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (17876) covalent geometry : angle 0.49641 / 0.26 (24216) hydrogen bonds : bond 0.03863 / 2.58 ( 1014) hydrogen bonds : angle 4.12326 / 2.92 ( 2940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 255 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6083 (mt) REVERT: A 316 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6468 (tp) REVERT: B 255 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6143 (mt) REVERT: B 478 GLU cc_start: 0.5731 (tt0) cc_final: 0.5435 (mt-10) REVERT: B 581 MET cc_start: 0.8582 (mmm) cc_final: 0.8221 (tpt) REVERT: B 642 THR cc_start: 0.8751 (t) cc_final: 0.8296 (p) REVERT: C 255 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6140 (mt) REVERT: C 316 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6398 (tp) REVERT: C 333 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6572 (tppt) REVERT: C 478 GLU cc_start: 0.5868 (tt0) cc_final: 0.5371 (tt0) REVERT: C 581 MET cc_start: 0.8554 (mmm) cc_final: 0.8191 (tpt) REVERT: C 642 THR cc_start: 0.8749 (t) cc_final: 0.8293 (p) REVERT: D 255 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6078 (mt) REVERT: D 472 TYR cc_start: 0.8116 (m-80) cc_final: 0.7852 (m-80) REVERT: D 478 GLU cc_start: 0.5728 (tt0) cc_final: 0.5433 (mt-10) REVERT: D 581 MET cc_start: 0.8552 (mmm) cc_final: 0.8185 (mmm) REVERT: D 642 THR cc_start: 0.8718 (t) cc_final: 0.8299 (p) outliers start: 25 outliers final: 5 residues processed: 236 average time/residue: 0.5840 time to fit residues: 153.5101 Evaluate side-chains 208 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 13 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 HIS A 688 ASN B 411 HIS B 688 ASN C 411 HIS C 688 ASN D 411 HIS D 688 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.215034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 154)---------------| | r_work = 0.3639 r_free = 0.3639 target = 0.146719 restraints weight = 15664.462| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.62 r_work: 0.3359 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17876 Z= 0.149 Angle : 0.538 6.677 24216 Z= 0.284 Chirality : 0.037 0.120 2716 Planarity : 0.004 0.040 2956 Dihedral : 5.039 41.103 2624 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.39 % Allowed : 17.29 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 2108 helix: 1.93 (0.14), residues: 1292 sheet: -2.11 (0.44), residues: 116 loop : -1.57 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 499 TYR 0.012 0.001 TYR A 584 PHE 0.017 0.002 PHE C 496 TRP 0.015 0.001 TRP B 698 HIS 0.006 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (17876) covalent geometry : angle 0.53829 / 0.28 (24216) hydrogen bonds : bond 0.04358 / 2.92 ( 1014) hydrogen bonds : angle 4.19280 / 2.96 ( 2940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 255 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6107 (mt) REVERT: A 316 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6451 (tp) REVERT: A 478 GLU cc_start: 0.6318 (tt0) cc_final: 0.5954 (mt-10) REVERT: A 581 MET cc_start: 0.8544 (mmm) cc_final: 0.8320 (mmm) REVERT: B 255 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6040 (mt) REVERT: B 478 GLU cc_start: 0.5641 (tt0) cc_final: 0.5076 (tt0) REVERT: B 581 MET cc_start: 0.8604 (mmm) cc_final: 0.8275 (mmm) REVERT: C 255 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.5958 (mt) REVERT: C 316 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6381 (tp) REVERT: C 333 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6619 (tppt) REVERT: C 478 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5635 (mt-10) REVERT: C 581 MET cc_start: 0.8603 (mmm) cc_final: 0.8248 (tpt) REVERT: D 255 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6173 (mt) REVERT: D 478 GLU cc_start: 0.5792 (tt0) cc_final: 0.5455 (mt-10) REVERT: D 581 MET cc_start: 0.8596 (mmm) cc_final: 0.8247 (tpt) outliers start: 26 outliers final: 16 residues processed: 217 average time/residue: 0.6022 time to fit residues: 146.2186 Evaluate side-chains 216 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 712 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 16 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 169 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 4 optimal weight: 0.0170 chunk 181 optimal weight: 2.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 HIS A 688 ASN B 411 HIS B 688 ASN C 411 HIS C 688 ASN D 411 HIS D 688 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.216364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.163789 restraints weight = 15559.665| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.31 r_work: 0.3393 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17876 Z= 0.124 Angle : 0.521 12.648 24216 Z= 0.274 Chirality : 0.036 0.118 2716 Planarity : 0.003 0.038 2956 Dihedral : 4.885 41.973 2624 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.28 % Allowed : 17.61 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 2108 helix: 2.08 (0.14), residues: 1296 sheet: -2.03 (0.44), residues: 116 loop : -1.44 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.010 0.001 TYR A 584 PHE 0.021 0.001 PHE D 305 TRP 0.014 0.001 TRP D 698 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (17876) covalent geometry : angle 0.52106 / 0.27 (24216) hydrogen bonds : bond 0.04075 / 2.73 ( 1014) hydrogen bonds : angle 4.13714 / 2.92 ( 2940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 255 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6172 (mt) REVERT: A 316 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6517 (tp) REVERT: A 478 GLU cc_start: 0.5991 (tt0) cc_final: 0.5732 (tt0) REVERT: B 255 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6234 (mt) REVERT: B 315 MET cc_start: 0.6801 (mmm) cc_final: 0.6535 (mmt) REVERT: B 478 GLU cc_start: 0.5639 (tt0) cc_final: 0.5313 (mt-10) REVERT: B 581 MET cc_start: 0.8590 (mmm) cc_final: 0.8264 (tpt) REVERT: C 255 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6233 (mt) REVERT: C 316 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6432 (tp) REVERT: C 333 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6610 (tppt) REVERT: C 478 GLU cc_start: 0.6100 (tt0) cc_final: 0.5620 (mt-10) REVERT: C 581 MET cc_start: 0.8588 (mmm) cc_final: 0.8248 (tpt) REVERT: D 255 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6255 (mt) REVERT: D 316 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6441 (tp) REVERT: D 320 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5569 (mp) REVERT: D 472 TYR cc_start: 0.8050 (m-80) cc_final: 0.7839 (m-80) REVERT: D 478 GLU cc_start: 0.5628 (tt0) cc_final: 0.5302 (mt-10) REVERT: D 581 MET cc_start: 0.8580 (mmm) cc_final: 0.8244 (tpt) REVERT: D 642 THR cc_start: 0.8753 (t) cc_final: 0.8337 (p) outliers start: 24 outliers final: 15 residues processed: 220 average time/residue: 0.5930 time to fit residues: 145.7868 Evaluate side-chains 216 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 712 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 HIS A 688 ASN B 411 HIS B 688 ASN C 411 HIS C 688 ASN D 411 HIS D 688 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.215701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3755 r_free = 0.3755 target = 0.157338 restraints weight = 15636.987| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.29 r_work: 0.3368 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17876 Z= 0.144 Angle : 0.540 12.331 24216 Z= 0.283 Chirality : 0.037 0.119 2716 Planarity : 0.004 0.040 2956 Dihedral : 4.953 41.397 2624 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.45 % Allowed : 17.61 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 2108 helix: 1.99 (0.14), residues: 1288 sheet: -2.01 (0.44), residues: 116 loop : -1.53 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 499 TYR 0.011 0.001 TYR A 584 PHE 0.018 0.002 PHE C 496 TRP 0.014 0.001 TRP B 698 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (17876) covalent geometry : angle 0.54027 / 0.28 (24216) hydrogen bonds : bond 0.04281 / 2.87 ( 1014) hydrogen bonds : angle 4.17079 / 2.94 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6470.29 seconds wall clock time: 110 minutes 48.88 seconds (6648.88 seconds total)